I've made quite a few changes in the software as well as the hardware of the digital frequency counting setup.

• The main change on the software side is that the custom C code that counts intervals between successive zero crossings and updates the frequency output now has a moving average capability - the window size is readily changable (by a macro in the first line of the code, which resides at /opt/rtcds/userapps/release/cds/c1/src/countZeroCrossingWindowed.c - however, changing the window size requires that the model be recompiled and restarted), and is currently set to 4096 because based on some empirical trials I did, this seemed to give me the frequency output with the least jitter, and also smaller systematic errors than in my earlier trials described here.
• The filter modules for both the X and Y channels now have 2 pole butterworth low pass filters with poles at 64Hz, 32Hz, 16Hz, 8Hz, 4Hz, 2Hz and 1Hz loaded. Again, based on my empirical trials, a combination of a moving average filter in the C code and the IIR filters after that worked best in terms of reducing the jitter in the frequency readout. I think the fact that the moving average 'spreads' the impulse caused by a glitch in the counting algorithm improves the response of the combination as compared to having only the IIR filters in place. 
• The Frequency Counting SIMULINK block has been cleaned up a little - I have removed unnecessary test points I had set up for debugging, and is now a library part called "FC".
• After the experience of having C1ALS crash as noted here, I was doing all my testing in the C1TST model. Having made all the changes above, I reverted to the C1ALS model, which compiled and ran successfully this time.
• On the hardware side, I interchanged the couplers mentioned here - so the 20dB coupler now sits on the X green beat PD, while the 10dB coupler sits on the Y green beat PD. This change was motivated by wanting to test out the digital frequency counting setup by performing an arm scan through an IR resonance using ALS, and we found that the PSL+Y green beat frequency was better behaved than the X+PSL combination.

Arm scan

Eric helped me test the new setup by doing an arm scan through an IR resonance by ramping the ALS offset from -3 to +3 with a ramp time of 45 seconds. The data was acquired with the window size of the moving average set to 4096 clock cycles, and a 2 Hz low pass IIR filter before the frequency readout. Attachment 1 shows a plot of the data, and a fit with a function of the form trans = a/(1+((x-b)/c)^2), where a = normalization, b = center of lorentzian, and c = linewidth (FWHM) of the peak (the fitted parameter values, along with 95% confidence bounds are also quoted on the plot). In terms of the data acquisition, comparing this dataset to one from an earlier scan Eric did (elog11111) suggests that the frequency counting setup is working reasonably well - at any rate, I think the data is a lot cleaner than before implementing the moving average and having a 20Hz lowpass IIR filter. In any case, we plan to repeat this measurement sometime next week during a nighttime locking session. It remains to calculate the arm loss from these numbers analogous to what was done earlier for the X arm.

Calculation of loss:

Fitted linewidth = 10.884 kHz +/- 11Hz (95% C.I.)

FSR of Y arm (from elog 9804) = 3.9468 MHz +/- 1.1 kHz

=> Y arm Finesse = FSR/fitted linewidth =  362.6 +/- 0.5

Total round trip loss = 2*pi/Finesse = 0.0173